[gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio rmbio861 at gmail.com
Wed Oct 21 16:46:11 CEST 2009

Dear Justin.

Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame  I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was

Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
All averages are exact over 500001 steps

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
Potential                -1.2189e+06    1115.54    1070.01    -1.0927    -1092.7

then I had a look at the PE.xvg file, but the values are very close to
identify the lowest energy point, i also tried to a have a look at the
md_0_1.log file, here also it is tedious and time consuming and the
values are close to remember. Can you suggest me how to locate the
lowest energy frame, so that i can use the comand (below) to retrieve
that particular frame coordinates in PDB file:

trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
number- corresponding to the lowest energy)

and also please tell the whether the command i am going to use to
retrieve the lowest energy configuration is correct.



On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> ram bio wrote:
>> Dear Justin,
>> Thanks for the suggestion and advice.
>> As i have used a modelled protein and want to obtain the lowest energy
>> configuration of the protein by doing dynamics, i want to collect the
>> structure (coordinates in pdb) representing average of all the
>> frames/configurations produced in MD and also the lowest energy
>> configuration structure (coordinates in PDB) produced during the
>> simulation, which can be used for docking. Please help how to obtain
>> the average structure as well as the lowest energy configuration
>> structure.
> Average structures are not always meaningful (or even physically-relevant):
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
> You can get average structures from, i.e. g_cluster -cl, if you want.  As
> for the lowest energy structure, analyze potential energy, and dump out the
> frame corresponding to the lowest point.  Hopefully you saved coordinates
> and energies at the same interval :)  The potential energy will correspond
> to that of the system, but hopefully it should give some indication of the
> lowest energy configuration.  I don't know anything about your system, but
> it will also depend on how much the energy fluctuates as to how relevant
> this structure might be, and how different it might be from an "average."
> If your structure comes from some model you built, realize that 1 ns is an
> exceptionally short time frame, especially given the capabilities of modern
> hardware and the speed of the GROMACS code.  You may want to consider
> running a bit longer to ensure that you really have a stable system.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list